Materials Physics Center - University of the Basque Country

General Information

Software Carpentry's mission
is to help scientists and engineers get more research done in less
time and with less pain by teaching them basic lab skills for
scientific computing. This hands-on workshop will cover basic
concepts and tools, including program design, version control, data
management, and task automation. Participants will be encouraged to
help one another and to apply what they have learned to their own
research problems.

Who:
The course is aimed at graduate students, post-doctoral researchers
and other researchers. Applicants from the organizing and collaborating
entities (CFM, IT Faculty Computational Intelligence Group and DIPC) will
have priority, but the course is open to all scientific community.

Introduction to Scientific Python

NumPy, SciPy, matplotlib

Setup

To participate in a Software Carpentry workshop, you will need
access to the software described below. In addition, you will
need an up-to-date web browser.
Once you are done installing the software listed below,
please go to this page,
which has instructions on how to test that everything was installed correctly.

Text Editor

When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it, try
typing the escape key, followed by ':q!' (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.

Windows

nano is the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
lesson material.

Notepad++ is a
popular free code editor for Windows. Be aware that you must
add its installation directory to your system path in order to
launch it from the command line (or have other tools like Git
launch it for you). Please ask your instructor to help you do
this.

Mac OS X

The default shell in all versions of Mac OS X is bash, so no
need to install anything. You access bash from the Terminal
(found in
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.

Git

Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser (current versions of Chrome, Firefox or Safari,
or Internet Explorer version 9 or above).

Windows

Git should be installed on your computer as part of your Bash
install (described above).

Mac OS X

For OS X 10.8 and higher, install Git for Mac
by downloading and running
the installer.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program.
For older versions of OS X (10.5-10.7) use the
most recent available installer for your
OS available
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.

Linux

If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git.

Python

Python is a popular language for
scientific computing, and great for general-purpose programming as
well. Installing all of its scientific packages individually can be
a bit difficult, so we recommend an all-in-one installer.

Regardless of how you choose to install it,
please make sure you install Python version 2.x and not version 3.x
(e.g., 2.7 is fine but not 3.4).
Python 3 introduced changes that will break some of the code we teach during the workshop.

We will teach Python using the IPython notebook, a programming environment
that runs in a web browser. For this to work you will need a reasonably
up-to-date browser. The current versions of the Chrome, Safari and
Firefox browsers are all supported
(some older browsers, including Internet Explorer version 9
and below, are not).

Mac OS X

Download the default Python 2 installer (do not follow the link to version 3).
Use all of the defaults for installation.

Linux

We recommend the all-in-one scientific Python installer
Anaconda.
(Installation requires using the shell and if you aren't
comfortable doing the installation yourself just
download the installer and we'll help you at the workshop.)

Download the installer that matches your operating
system and save it in your home folder.
Download the default Python 2 installer (do not follow the link to version 3).

Open a terminal window.

Type

bash Anaconda-

and then press
tab. The name of the file you just downloaded should
appear.

Press enter. You will follow the text-only prompts. When
there is a colon at the bottom of the screen press the down
arrow to move down through the text. Type yes and
press enter to approve the license. Press enter to approve the
default location for the files. Type yes and
press enter to prepend Anaconda to your PATH
(this makes the Anaconda distribution the default Python).